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###
### Running command:
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### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL Biostrings
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘Biostrings’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c BAB_class.c -o BAB_class.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c BitMatrix.c -o BitMatrix.o
BitMatrix.c:299:13: warning: ‘BitMatrix_print’ defined but not used [-Wunused-function]
299 | static void BitMatrix_print(BitMatrix *bitmat)
| ^~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function ‘SparseMIndex_endIndex’:
MIndex_class.c:184:20: warning: unused variable ‘poffsets_order’ [-Wunused-variable]
184 | IntAE *poffsets, *poffsets_order;
| ^~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c XStringSetList_class.c -o XStringSetList_class.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function ‘new_XStringSet_from_CHARACTER’:
XStringSet_class.c:124:3: warning: ‘lkup_len’ may be used uninitialized in this function [-Wmaybe-uninitialized]
124 | _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
125 | INTEGER(start)[i], lkup0, lkup_len);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c XString_class.c -o XString_class.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function ‘align_needwunsQS’:
align_needwunsQS.c:155:22: warning: ‘sc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
155 | INTEGER(ans_elt)[0] = score;
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c align_utils.c -o align_utils.o
align_utils.c: In function ‘PairwiseAlignmentsSingleSubject_align_aligned’:
align_utils.c:250:14: warning: ‘indelWidthSubject’ may be used uninitialized in this function [-Wmaybe-uninitialized]
250 | jPattern += indelWidthSubject;
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:231:42: warning: ‘indelStartSubject’ may be used uninitialized in this function [-Wmaybe-uninitialized]
231 | if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
| ~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:221:26: warning: ‘indelWidthPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
221 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
| ^~~~~~~~~~~~~~~~~
align_utils.c:232:50: warning: ‘indelStartPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
232 | if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_palindromes.c -o find_palindromes.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c gtestsim.c -o gtestsim.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c inject_code.c -o inject_code.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c letter_frequency.c -o letter_frequency.o
letter_frequency.c: In function ‘XStringSet_two_way_letter_frequency’:
letter_frequency.c:957:48: warning: unused variable ‘x_pos’ [-Wunused-variable]
957 | int x_width, y_width, x_length, *ans_mat, i, x_pos;
| ^~~~~
letter_frequency.c:956:13: warning: unused variable ‘ans_dimnames’ [-Wunused-variable]
956 | SEXP ans, ans_dimnames;
| ^~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c lowlevel_matching.c -o lowlevel_matching.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_PWM.c -o match_PWM.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pattern.c -o match_pattern.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pattern_indels.c -o match_pattern_indels.o
match_pattern_indels.c:7:13: warning: ‘test_match_pattern_indels’ defined but not used [-Wunused-function]
7 | static void test_match_pattern_indels(const char *p, const char *s,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pdict.c -o match_pdict.o
match_pdict.c: In function ‘vmatch_PDict3Parts_XStringSet’:
match_pdict.c:419:12: warning: ‘ans_col’ may be used uninitialized in this function [-Wmaybe-uninitialized]
419 | ans_col += tb_length;
| ~~~~~~~~^~~~~~~~~~~~
match_pdict.c:392:58: note: ‘ans_col’ was declared here
392 | int tb_length, S_length, collapse0, i, j, match_count, *ans_col;
| ^~~~~~~
match_pdict.c: In function ‘vmatch_XStringSet_XStringSet’:
match_pdict.c:470:13: warning: ‘ans_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
470 | ans_elt += P_length;
| ~~~~~~~~^~~~~~~~~~~
match_pdict.c:441:57: note: ‘ans_elt’ was declared here
441 | int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
| ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c: In function ‘split_and_move_pointers’:
match_pdict_ACtree2.c:1031:10: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable]
1031 | ACnode *node0, *node1, *node2;
| ^~~~~
match_pdict_ACtree2.c: In function ‘merge_pointers’:
match_pdict_ACtree2.c:1076:10: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable]
1076 | ACnode *node0, *node1, *node2;
| ^~~~~
At top level:
match_pdict_ACtree2.c:602:21: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used [-Wunused-function]
602 | static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
match_pdict_ACtree2.c:139:13: warning: ‘debug_node_counting_functions’ defined but not used [-Wunused-function]
139 | static void debug_node_counting_functions(int maxdepth)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function ‘build_Twobit’:
match_pdict_Twobit.c:75:20: warning: ‘twobit_sign2pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
75 | PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos));
| ^~~~~~~~~~~~~~~~~~~~~
match_pdict_Twobit.c:110:12: note: ‘twobit_sign2pos’ was declared here
110 | SEXP ans, twobit_sign2pos;
| ^~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function ‘match_ppheadtail0’:
match_pdict_utils.c:652:49: warning: unused variable ‘ncol’ [-Wunused-variable]
652 | int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
| ^~~~
match_pdict_utils.c: In function ‘match_ppheadtail’:
match_pdict_utils.c:712:6: warning: unused variable ‘nelt’ [-Wunused-variable]
712 | int nelt, nkey0, nkey1, nkey2, i, key;
| ^~~~
match_pdict_utils.c: In function ‘_match_pdict_all_flanks’:
match_pdict_utils.c:819:44: warning: unused variable ‘subtotal_NFC’ [-Wunused-variable]
819 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
| ^~~~~~~~~~~~
match_pdict_utils.c:819:27: warning: unused variable ‘total_NFC’ [-Wunused-variable]
819 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
| ^~~~~~~~~
match_pdict_utils.c:818:33: warning: unused variable ‘NFC’ [-Wunused-variable]
818 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
| ^~~
match_pdict_utils.c:818:26: warning: unused variable ‘nloci’ [-Wunused-variable]
818 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
| ^~~~~
match_pdict_utils.c:818:20: warning: unused variable ‘ndup’ [-Wunused-variable]
818 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
| ^~~~
At top level:
match_pdict_utils.c:819:27: warning: ‘total_NFC’ defined but not used [-Wunused-variable]
819 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
| ^~~~~~~~~
match_pdict_utils.c:819:44: warning: ‘subtotal_NFC’ defined but not used [-Wunused-variable]
819 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
| ^~~~~~~~~~~~
match_pdict_utils.c:260:13: warning: ‘match_headtail_by_loc’ defined but not used [-Wunused-function]
260 | static void match_headtail_by_loc(const HeadTail *headtail,
| ^~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c match_reporting.c -o match_reporting.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c matchprobes.c -o matchprobes.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c read_fasta_files.c -o read_fasta_files.o
read_fasta_files.c: In function ‘read_fasta_files’:
read_fasta_files.c:186:9: warning: ‘*((void *)&loader_ext+64)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
186 | return loader_ext;
| ^~~~~~~~~~
read_fasta_files.c:186:9: warning: ‘*((void *)&loader_ext+72)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
read_fasta_files.c: In function ‘read_fasta_blocks’:
read_fasta_files.c:186:9: warning: ‘*((void *)&loader_ext+64)’ is used uninitialized in this function [-Wuninitialized]
186 | return loader_ext;
| ^~~~~~~~~~
read_fasta_files.c:186:9: warning: ‘*((void *)&loader_ext+72)’ is used uninitialized in this function [-Wuninitialized]
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c read_fastq_files.c -o read_fastq_files.o
read_fastq_files.c: In function ‘parse_FASTQ_file’:
read_fastq_files.c:392:7: warning: ‘dont_load’ may be used uninitialized in this function [-Wmaybe-uninitialized]
392 | if (dont_load || loader->new_empty_seq_hook == NULL)
| ^
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c replaceAt.c -o replaceAt.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c replace_letter_at.c -o replace_letter_at.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c strutils.c -o strutils.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c translate.c -o translate.o
translate.c: In function ‘DNAStringSet_translate’:
translate.c:110:8: warning: ‘if_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
110 | if (if_ambig == TRANSLATE_ERROR) {
| ^
translate.c:136:29: note: ‘if_ambig0’ was declared here
136 | int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
| ^~~~~~~~~
translate.c:106:8: warning: ‘if_non_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
106 | if (if_non_ambig == TRANSLATE_TO_X)
| ^
translate.c:136:14: note: ‘if_non_ambig0’ was declared here
136 | int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
| ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o
utils.c: In function ‘_get_twobit_signature’:
utils.c:157:9: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized]
157 | return twobit_sign;
| ^~~~~~~~~~~
utils.c: In function ‘_get_twobit_signature_at’:
utils.c:164:12: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized]
164 | int i, j, twobit_sign;
| ^~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c xscat.c -o xscat.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include/IRanges_defines.h:18,
from ../inst/include/Biostrings_defines.h:18,
from Biostrings.h:1,
from xscat.c:1:
xscat.c: In function ‘XString_xscat’:
/home/biocbuild/bbs-3.14-bioc/R/include/Rdefines.h:100:21: warning: ‘ans_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
100 | #define NEW_RAW(n) Rf_allocVector(RAWSXP,n)
| ^~~~~~~~~~~~~~
xscat.c:18:13: note: ‘ans_length’ was declared here
18 | int nargs, ans_length, tag_offset, j;
| ^~~~~~~~~~
xscat.c:52:16: warning: ‘ans_classname’ may be used uninitialized in this function [-Wmaybe-uninitialized]
52 | PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag));
| ^~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include/IRanges_defines.h:18,
from ../inst/include/Biostrings_defines.h:18,
from Biostrings.h:1,
from xscat.c:1:
xscat.c: In function ‘XStringSet_xscat’:
/home/biocbuild/bbs-3.14-bioc/R/include/Rdefines.h:94:25: warning: ‘ans_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
94 | #define NEW_INTEGER(n) Rf_allocVector(INTSXP,n)
| ^~~~~~~~~~~~~~
xscat.c:66:32: note: ‘ans_length’ was declared here
66 | int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
| ^~~~~~~~~~
xscat.c:108:16: warning: ‘ans_element_type’ may be used uninitialized in this function [-Wmaybe-uninitialized]
108 | PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width));
| ^~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-Biostrings/00new/Biostrings/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘twoWayAlphabetFrequencyByQuality’ with signature ‘"QualityScaledXStringSet"’: no definition for class “QualityScaledXStringSet”
Creating a new generic function for ‘strsplit’ in package ‘Biostrings’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’
Creating a new generic function for ‘pattern’ in package ‘Biostrings’
Creating a new generic function for ‘offset’ in package ‘Biostrings’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Biostrings)
